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standard-bin.json
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{
"bin": {
"exomeseq": {
"NOVOALIGN": "/usr/local/apps/novocraft/3.04.04/novoalign",
"NOVOSORT": "/usr/local/apps/novocraft/3.04.04/novosort",
# "ANNOVAR1": "/usr/local/apps/ANNOVAR/2014-07-14/convert2annovar.pl",
# "ANNOVAR2": "/usr/local/apps/ANNOVAR/2014-07-14/table_annovar.pl",
"ANNOVAR1": "/usr/local/apps/ANNOVAR/2015-03-22/convert2annovar.pl",
"ANNOVAR2": "/usr/local/apps/ANNOVAR/2015-03-22/table_annovar.pl",
"INDEXBAM": "java -jar /usr/local/apps/picard/1.129/picard.jar BuildBamIndex",
# "COVCALC": "QC/Coverage_calc4.pl",
# "COVFREQ": "/data/CCBR_Pipeliner/local/lib/Cov_Frequency_targeted.R",
"GATK": "java -Xmx64g -jar /usr/local/apps/GATK/3.5-0/GenomeAnalysisTK.jar",
"MARKDUPS": "module load picard/2.1.1; java -Xmx16g -XX:ParallelGCThreads=12 -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar MarkDuplicates",
"PICARD1": "module load picard/2.1.1; java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar AddOrReplaceReadGroups",
"PICARD2": "module load picard/2.1.1; java -Xmx4G -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar CollectInsertSizeMetrics",
"PICARD3": "/ngs/bin/jdk1.8.0_25/bin/java -jar /ngs/bin/picard-tools-1.119/CreateSequenceDictionary.jar",
# "PICHIST": "/data/CCBR_Pipeliner/local/lib/picardhist.R",
# "QCAL": "/data/CCBR_Pipeliner/local/lib/qcalplot.R",
# "READDIST": "/data/CCBR_Pipeliner/local/lib/ReadDist.R",
"VARSCAN": "java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/varscan/2.3.6/VarScan.v2.3.6.jar",
"NGSQCTOOLKIT": "/usr/local/apps/ngsqctoolkit/2.3.3/QC/IlluQC.pl",
"TRIMMOMATIC": "java -Xmx2g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/trimmomatic/Trimmomatic-0.33/trimmomatic-0.33.jar",
# "FASTQC": "export JAVA_OPTS='-Djava.io.tmpdir=/lscratch/$SLURM_JOBID; /usr/local/apps/fastqc/0.11.5/fastqc",
"FASTQC": "/usr/local/apps/fastqc/0.11.5/fastqc",
"SAMTOOLS": "/usr/local/apps/samtools/1.3.1/bin/samtools",
"BAMTOOLS": "/usr/local/apps/bamtools/2.3.0/bin/bamtools",
"BEDTOOLS": "/usr/local/apps/bedtools/2.19.0/bin/bedtools",
"QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/$SLURM_JOBID'; /usr/local/apps/qualimap/qualimap_v2.2.1/qualimap --java-mem-size=96G",
"STAR": "/usr/local/apps/STAR/2.4.0h/bin/Linux_x86_64/STAR",
"SNPEFF": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/snpEff.jar",
"SNPSIFT": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/SnpSift.jar",
"FIRSTANNO": "Scripts/vcfAnnFirst_snpEff.py",
"MUTECT": "module load java/1.7.0_25; java -Xmx16g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/muTect/2014-12-15/muTect-1.1.7.jar",
# "SVDETECT": "/data/CCBR_Pipeliner/local/apps",
# "BICSEQ": "/data/CCBR_Pipeliner/local/apps/BIC-seq.pl",
"BWA": "/usr/local/apps/bwa/0.7.15/bwa",
"FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen"
},
"genomeseq": {
"NOVOALIGN": "/usr/local/apps/novocraft/3.04.04/novoalign",
"NOVOSORT": "/usr/local/apps/novocraft/3.04.04/novosort",
# "ANNOVAR1": "/usr/local/apps/ANNOVAR/2014-07-14/convert2annovar.pl",
# "ANNOVAR2": "/usr/local/apps/ANNOVAR/2014-07-14/table_annovar.pl",
"ANNOVAR1": "/usr/local/apps/ANNOVAR/2015-03-22/convert2annovar.pl",
"ANNOVAR2": "/usr/local/apps/ANNOVAR/2015-03-22/table_annovar.pl",
"INDEXBAM": "java -jar /usr/local/apps/picard/1.129/picard.jar BuildBamIndex",
# "COVCALC": "QC/Coverage_calc4.pl",
# "COVFREQ": "/data/CCBR_Pipeliner/local/lib/Cov_Frequency_targeted.R",
"GATK": "java -Xmx64g -jar /usr/local/apps/GATK/3.5-0/GenomeAnalysisTK.jar",
"MARKDUPS": "module load picard/2.1.1; java -Xmx16g -XX:ParallelGCThreads=12 -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar MarkDuplicates",
"PICARD1": "module load picard/2.1.1; java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar AddOrReplaceReadGroups",
"PICARD2": "module load picard/2.1.1; java -Xmx4G -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar CollectInsertSizeMetrics",
"PICARD3": "/ngs/bin/jdk1.8.0_25/bin/java -jar /ngs/bin/picard-tools-1.119/CreateSequenceDictionary.jar",
# "PICHIST": "/data/CCBR_Pipeliner/local/lib/picardhist.R",
# "QCAL": "/data/CCBR_Pipeliner/local/lib/qcalplot.R",
# "READDIST": "/data/CCBR_Pipeliner/local/lib/ReadDist.R",
"VARSCAN": "java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/varscan/2.3.6/VarScan.v2.3.6.jar",
"NGSQCTOOLKIT": "/usr/local/apps/ngsqctoolkit/2.3.3/QC/IlluQC.pl",
"TRIMMOMATIC": "java -Xmx2g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/trimmomatic/Trimmomatic-0.33/trimmomatic-0.33.jar",
# "FASTQC": "export JAVA_OPTS='-Djava.io.tmpdir=/lscratch/$SLURM_JOBID; /usr/local/apps/fastqc/0.11.5/fastqc",
"FASTQC": "/usr/local/apps/fastqc/0.11.5/fastqc",
"SAMTOOLS": "/usr/local/apps/samtools/1.3.1/bin/samtools",
"BAMTOOLS": "/usr/local/apps/bamtools/2.3.0/bin/bamtools",
"BEDTOOLS": "/usr/local/apps/bedtools/2.19.0/bin/bedtools",
"QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/$SLURM_JOBID'; /usr/local/apps/qualimap/qualimap_v2.2/qualimap --java-mem-size=64G",
"STAR": "/usr/local/apps/STAR/2.4.0h/bin/Linux_x86_64/STAR",
"SNPEFF": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/snpEff.jar",
"SNPSIFT": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/SnpSift.jar",
"FIRSTANNO": "Scripts/vcfAnnFirst_snpEff.py",
"MUTECT": "module load java/1.7.0_25; java -Xmx16g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/muTect/2014-12-15/muTect-1.1.7.jar",
# "SVDETECT": "/data/CCBR_Pipeliner/local/apps",
# "BICSEQ": "/data/CCBR_Pipeliner/local/apps/BIC-seq.pl",
"BWA": "/usr/local/apps/bwa/0.7.15/bwa",
"FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen"
},
"rnaseq": {
"tool_versions": {
"BOWTIE2VER" : "bowtie/2-2.3.4",
"BWAVER": "bwa/0.7.17",
"CUTADAPTVER": "cutadapt/1.18",
"FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen",
"FASTQCVER" : "fastqc/0.11.5",
"KRAKENVER": "kraken/1.1",
"KRONATOOLSVER": "kronatools/2.7",
"MULTIQCVER":"multiqc/1.4",
"PARALLELVER" : "parallel/20171222",
"PERLVER" : "perl/5.24.3",
"PICARDVER" : "picard/2.17.11",
# "PIGZVER" : "pigz/2.3.4",
"PRESEQVER": "preseq/2.0.3",
"PYTHONVER" : "python/3.5",
"RMATSVER" : "rmats/4.0.1",
"RSEMVER" : "rsem/1.3.0",
"RSEQCVER" : "rseqc/2.6.4",
"RVER" : "R/3.5",
"SAMTOOLSVER" : "samtools/1.6",
"STARVER": "STAR/2.7.0f",
"SUBREADVER": "subread/1.5.2",
"TRIMMOMATICVER": "trimmomatic/0.33",
},
"tool_parameters":{
"FASTAWITHADAPTERSETC" : "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"FASTAWITHADAPTERSETD" : "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.consolidated.fa",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"FASTQ_SCREEN_CONFIG2": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen_2.conf",
"KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
"Trimsettings": "---------------------------- TRIMMOMATIC parameters ----------------------------------------------------------",
"SEEDMISMATCHES": 2,
"PALINDROMECLIPTHRESHOLD": 36,
"SIMPLECLIPTHRESHOLD": 10,
"LEADINGQUALITY": 10,
"TRAILINGQUALITY": 10,
"CROPLENGTH": 0,
"HEADCROPLENGTH": 0,
"MINLEN": 35,
"TARGETLENGTH": 50,
"STRICTNESS": 0.97,
"WINDOWSIZE": 4,
"WINDOWQUALITY": 27,
},
"FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen",
"ONCOFUSE": "java -Xmx24g -jar /data/CCBR_Pipeliner/db/PipeDB/bin/oncofuse-1.1.1/Oncofuse.jar",
"PYTHONPATH": "/data/CCBR_Pipeliner/db/PipeDB/bin/lib/python3.4/site-packages/",
"MULTIQC":"multiqc/1.1",
"CONFMULTIQC": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/multiqc/multiqc_config.yaml",
"TRIMMOMATICVER": "trimmomatic/0.33",
"FASTQCVER": "fastqc",
"CHKQCVER": " /data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/summarizeFastQCver2",
"STARVER": "STAR/2.5.2b",
"SUBREADVER": "subread/1.5.2",
"BWAVER": "bwa/0.7.17",
"RNASEQCJAR": "/usr/local/apps/rnaseqc/1.1.8/RNA-SeQC_v1.1.8.jar",
"IOoptions": "--------------------------- Output and input locations ---------------------------------------------------------",
"MYFOLDER": "/scratch/nikhil/731/",
"INPUTDIR": "/scratch/nikhil/731/fastq/",
"SamplesInformation": "-------------sample list & contrasts information --------------------------------------------------------",
"MYSAMPLES": ["12284_N_S38","12284_T_S37","21238_N_S42","21238_T_S41","23709_N_S40","23709_T_S39"],
"GROUPS": ["Normal","Tumor","Normal","Tumor","Normal","Tumor"],
"CONTRASTS": ["Normal","Tumor"],
"Options": "---------------------------------- Branching options --------------------------------------------------------------",
"TRIM": "yes",
"DEG": "yes",
"RESUME": "no",
"Trimsettings": "---------------------------- TRIMMOMATIC parameters ----------------------------------------------------------",
"SEEDMISMATCHES": 2,
"PALINDROMECLIPTHRESHOLD": 36,
"SIMPLECLIPTHRESHOLD": 10,
"LEADINGQUALITY": 10,
"TRAILINGQUALITY": 10,
"CROPLENGTH": 0,
"HEADCROPLENGTH": 0,
"MINLEN": 35,
"TARGETLENGTH": 50,
"STRICTNESS": 0.97,
"WINDOWSIZE": 4,
"WINDOWQUALITY": 27,
"Starsettings": "------------------------- STAR version and parameters ---------------------------------------------------------",
"SJDBOVERHANG": 125,
"OUTSAMUNMAPPED": "Within",
"ADAPTER1": "-",
"ADAPTER2": "",
"A1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"A2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
"STARSTRANDCOL": 4,
"NBJUNCS": 4000000,
"cufflinks": "-------------------------Cufflinks options (for now defaults)----------------------------------------------------",
"FILTERINTRONMOTIFS": "RemoveNoncanonicalUnannotated",
"SAMSTRANDFIELD": "None",
"Encode": "-----------------------Encode options (for now we have defaults except first) --------------------------------------",
"FILTERTYPE": "BySJout",
"FILTERMULTIMAPNMAX": 20,
"ALIGNSJOVERHANGMIN": 8,
"ALIGNSJDBOVERHANGMIN": 1,
"FILTERMISMATCHNMAX": 999,
"FILTERMISMATCHNOVERLMAX": 0.3,
"ALIGNINTRONMIN": 20,
"ALIGNINTRONMAX": 1000000,
"ALIGNMATESGAPMAX": 1000000,
"wig": "------------------------------------wig options (for now default) ------------------------------------------------------",
"WIGTYPE": "None",
"WIGSTRAND": "Stranded",
"Picardsettings": "------------------------- PICARD options --------------------------------------------------------------------",
"PICARDSTRAND": "SECOND_READ_TRANSCRIPTION_STRAND",
"subreadsettings": "---------------------- SUBREAD parameters ------------------------------------------------------------------",
"strandinfo": "-[SUBREAD STRANDEDNESS: 0=unstranded--1=stranded--2=reverse-strand-specific]- ",
"STRANDED": 2,
"mincountinfo": "------------------------------Min count thresholds-------------------------------------------------------------",
"MINCOUNTGENES": 5,
"MINCOUNTJUNCTIONS": 5,
"MINCOUNTGENEJUNCTIONS": 5,
"MINSAMPLES": 1,
"PIPERLIB": "/data/CCBR_Pipeliner/db/PipeDB/R2/",
"RSEM": "/usr/local/apps/rsem/1.3.0",
"FASTQC": "/usr/local/apps/fastqc/0.11.5/fastqc",
"GATK": "java -Xmx64g -jar /usr/local/apps/GATK/3.5-0/GenomeAnalysisTK.jar",
"SAMTOOLS": "/usr/local/apps/samtools/1.6/bin/samtools",
"PICARD3": "/ngs/bin/jdk1.8.0_25/bin/java -jar /ngs/bin/picard-tools-1.119/CreateSequenceDictionary.jar",
"NGSQCTOOLKIT": "/usr/local/apps/ngsqctoolkit/2.3.3/QC/IlluQC.pl",
"NOVOSORT": "/usr/local/apps/novocraft/3.08.02/novosort",
"PICARD1": "module load picard/2.17.11; java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar AddOrReplaceReadGroups",
"MARKDUPS": "module load picard/2.17.11; java -Xmx16g -XX:ParallelGCThreads=12 -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar MarkDuplicates",
"QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/$SLURM_JOBID'; /usr/local/apps/qualimap/qualimap_v2.2.1/qualimap --java-mem-size=64G",
"SNPEFF": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.3t/snpEff.jar",
"TRIMMOMATIC": "java -Xmx8g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/trimmomatic/Trimmomatic-0.33/trimmomatic-0.33.jar",
},
"rnaseqvargerm": {
"NOVOALIGN": "/usr/local/apps/novocraft/3.04.04/novoalign",
"NOVOSORT": "/usr/local/apps/novocraft/3.04.04/novosort",
"ANNOVAR1": "/usr/local/apps/ANNOVAR/2015-03-22/convert2annovar.pl",
"ANNOVAR2": "/usr/local/apps/ANNOVAR/2015-03-22/table_annovar.pl",
"INDEXBAM": "java -jar /usr/local/apps/picard/1.129/picard.jar BuildBamIndex",
"GATK": "java -Xmx64g -jar /usr/local/apps/GATK/3.6/GenomeAnalysisTK.jar",
"MARKDUPS": "module load picard/2.1.1; java -Xmx16g -XX:ParallelGCThreads=12 -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar MarkDuplicates",
"PICARD1": "module load picard/2.1.1; java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar AddOrReplaceReadGroups",
"PICARD2": "module load picard/2.1.1; java -Xmx4G -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar $PICARDJARPATH/picard.jar CollectInsertSizeMetrics",
"PICARD3": "/ngs/bin/jdk1.8.0_25/bin/java -jar /ngs/bin/picard-tools-1.119/CreateSequenceDictionary.jar",
"VARSCAN": "java -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/varscan/2.3.6/VarScan.v2.3.6.jar",
"NGSQCTOOLKIT": "/usr/local/apps/ngsqctoolkit/2.3.3/QC/IlluQC.pl",
"TRIMMOMATIC": "java -Xmx8g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/trimmomatic/Trimmomatic-0.33/trimmomatic-0.33.jar",
"FASTQC": "/usr/local/apps/fastqc/0.11.5/fastqc",
"SAMTOOLS": "/usr/local/apps/samtools/1.3.1/bin/samtools",
"BAMTOOLS": "/usr/local/apps/bamtools/2.3.0/bin/bamtools",
"BEDTOOLS": "/usr/local/apps/bedtools/2.19.0/bin/bedtools",
"QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/$SLURM_JOBID'; /usr/local/apps/qualimap/qualimap_v2.2/qualimap --java-mem-size=64G",
"STAR": "/usr/local/apps/STAR/2.4.0h/bin/Linux_x86_64/STAR",
"SNPEFF": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/snpEff.jar",
"SNPSIFT": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/SnpSift.jar",
"FIRSTANNO": "Scripts/vcfAnnFirst_snpEff.py",
"MUTECT": "module load java/1.7.0_25; java -Xmx16g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/muTect/2014-12-15/muTect-1.1.7.jar",
"BWA": "/usr/local/apps/bwa/0.7.15/bwa",
"FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen",
"PYTHONPATH": "/data/CCBR_Pipeliner/db/PipeDB/bin/lib/python3.4/site-packages/",
"MULTIQC":"multiqc/0.9dev0",
"CONFMULTIQC": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/multiqc_config.yaml",
"TRIMMOMATICVER": "trimmomatic/0.33",
"FASTQCVER": "fastqc",
"CHKQCVER": " /data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/summarizeFastQCver2",
"STARVER": "STAR/2.5.2b",
"PICARDVER": "picard/1.119",
"SUBREADVER": "subread/1.4.6",
"BWAVER": "bwa/0.7.10",
"RNASEQCVER": "/usr/local/apps/rnaseqc/1.1.8/RNA-SeQC_v1.1.8.jar",
"IOoptions": "--------------------------- Output and input locations ---------------------------------------------------------",
"MYFOLDER": "/scratch/nikhil/731/",
"INPUTDIR": "/scratch/nikhil/731/fastq/",
"SamplesInformation": "-------------sample list & contrasts information --------------------------------------------------------",
"MYSAMPLES": ["12284_N_S38","12284_T_S37","21238_N_S42","21238_T_S41","23709_N_S40","23709_T_S39"],
"GROUPS": ["Normal","Tumor","Normal","Tumor","Normal","Tumor"],
"CONTRASTS": ["Normal","Tumor"],
"Options": "---------------------------------- Branching options --------------------------------------------------------------",
"TRIM": "yes",
"DEG": "yes",
"RESUME": "no",
"Trimsettings": "---------------------------- TRIMMOMATIC parameters ----------------------------------------------------------",
"SEEDMISMATCHES": 2,
"PALINDROMECLIPTHRESHOLD": 36,
"SIMPLECLIPTHRESHOLD": 10,
"LEADINGQUALITY": 10,
"TRAILINGQUALITY": 10,
"CROPLENGTH": 0,
"HEADCROPLENGTH": 0,
"MINLEN": 20,
"TARGETLENGTH": 50,
"STRICTNESS": 0.97,
"WINDOWSIZE": 4,
"WINDOWQUALITY": 27,
"Starsettings": "------------------------- STAR version and parameters ---------------------------------------------------------",
"SJDBOVERHANG": 125,
"OUTSAMUNMAPPED": "Within",
"ADAPTER1": "-",
"ADAPTER2": "",
"A1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"A2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
"STARSTRANDCOL": 4,
"NBJUNCS": 4000000,
"cufflinks": "-------------------------Cufflinks options (for now defaults)----------------------------------------------------",
"FILTERINTRONMOTIFS": "RemoveNoncanonicalUnannotated",
"SAMSTRANDFIELD": "None",
"Encode": "-----------------------Encode options (for now we have defaults except first) --------------------------------------",
"FILTERTYPE": "BySJout",
"FILTERMULTIMAPNMAX": 20,
"ALIGNSJOVERHANGMIN": 8,
"ALIGNSJDBOVERHANGMIN": 1,
"FILTERMISMATCHNMAX": 999,
"FILTERMISMATCHNOVERLMAX": 0.3,
"ALIGNINTRONMIN": 20,
"ALIGNINTRONMAX": 1000000,
"ALIGNMATESGAPMAX": 1000000,
"wig": "------------------------------------wig options (for now default) ------------------------------------------------------",
"WIGTYPE": "None",
"WIGSTRAND": "Stranded",
"Picardsettings": "------------------------- PICARD options --------------------------------------------------------------------",
"PICARDSTRAND": "SECOND_READ_TRANSCRIPTION_STRAND",
"subreadsettings": "---------------------- SUBREAD parameters ------------------------------------------------------------------",
"strandinfo": "-[SUBREAD STRANDEDNESS: 0=unstranded--1=stranded--2=reverse-strand-specific]- ",
"STRANDED": 2,
"mincountinfo": "------------------------------Min count thresholds-------------------------------------------------------------",
"MINCOUNTGENES": 5,
"MINCOUNTJUNCTIONS": 5,
"MINCOUNTGENEJUNCTIONS": 5,
"MINSAMPLES": 1,
"PIPERLIB": "/data/CCBR_Pipeliner/db/PipeDB/R2/",
"RSEM": "/data/CCBR_Pipeliner/db/PipeDB/bin/rsem1.2.23/RSEM-1.2.23",
},
"ChIPseq":{
"tool_versions":{
"BEDTOOLSVER": "bedtools/2.27.1",
"BOWTIE2VER": "bowtie/2-2.3.4",
"BWAVER": "bwa/0.7.17",
"CUTADAPTVER": "cutadapt/1.18",
"DEEPTOOLSVER": "deeptools/3.0.1",
"FASTQCVER": "fastqc/0.11.5",
"GEMVER": "gem/3.0",
"HOMERVER": "homer/4.10.1",
"IDRVER": "idr/2.0.3",
"KRAKENVER": "kraken/1.1",
"KRONATOOLSVER": "kronatools/2.7",
"MACSVER": "macs/2.1.1.20160309",
"MULTIQCVER":"multiqc/1.7",
"PERLVER": "perl/5.24.3",
"PICARDVER": "picard/2.17.11",
"PRESEQVER": "preseq/2.0.3",
"RVER": "R/3.5",
"SAMTOOLSVER": "samtools/1.6",
"SICERVER": "sicer/1.1",
"UCSCVER": "ucsc/384",
"UROPAVER": "uropa/2.0.3",
},
"CONFMULTIQC": "/data/CCBR_Pipeliner/db/PipeDB/ChIPseq/multiqc_config.yaml",
"FASTAWITHADAPTERSETD" : "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.consolidated.fa",
"FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"FASTQ_SCREEN_CONFIG2": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen_2.conf",
"GEMREADDIST": '/usr/local/apps/gem/3.0/Read_Distribution_default.txt',
"KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
"NGSQC": "/data/CCBR_Pipeliner/db/PipeDB/ChIPseq/NGSQC_linux_x86_64",
},
"mirseq":{
"tool_versions": {
"FASTQCVER": "fastqc/0.11.5",
"CUTADAPTVER": "cutadapt/1.18",
"KRAKENVER": "kraken/1.1",
"KRONATOOLSVER": "kronatools/2.7",
"FASTXTOOLKITVER": "fastxtoolkit/0.0.14",
"FASTQ_SCREEN": "/data/CCBR_Pipeliner/db/PipeDB/bin/fastq_screen_v0.9.3/fastq_screen",
"BOWTIE2VER": "bowtie/2-2.3.4",
"PERLVER": "perl/5.24.3",
"MULTIQCVER": "multiqc/1.4",
"MIRDEEP2VER": "mirdeep/2.0.0.8"
},
"tool_paths":{
"SCRIPT_PATH": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/scripts",
"MIRDEEP2_PATH": "/usr/local/apps/mirdeep/2.0.0.7/bin",
"BOWTIE_PATH": "/usr/local/apps/bowtie/1.1.1",
"RANDFOLD_PATH": "/usr/local/apps/randfold/2.0/bin",
"SQUID_PATH": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/bin",
"PDFAPI2_PM_PATH": "/usr/share/perl5",
"NGS_PORTAL_PATH": "/projects/bsi/bictools/apps/misc/ngs_dashboard/2.0",
"JAVA_PATH": "/usr/bin",
"VIENNA_PATH": "/usr/local/apps/viennarna/2.1.9/bin",
"PICARD_PATH": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/bin/picard-tools-1.96",
"FASTQC_PATH": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/bin",
"CUTADAPT_PATH": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/bin",
"SAMTOOLS_PATH": "/usr/local/apps/samtools/samtools-0.1.19",
"BEDTOOLS_PATH": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/bin",
"GATK_JAR": "/usr/local/apps/GATK/3.3-0/GenomeAnalysisTK.jar",
"VCFTOOLS_PATH": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/bin",
"VCFTOOLS_PERLLIB": "/usr/local/apps/vcftools/0.1.12b/perl/",
"HTSEQ_PATH": "/usr/local/apps/htseq/0.6.1p1/bin",
"HTSEQ_LIB_PATH": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/HTSeq-0.5.4p5-py2.7-linux-x86_64.egg",
"PYTHON_PATH": "/usr/local/Anaconda/envs/py2.7.9/bin",
"RSCRIPT_PATH": "/usr/local/apps/R/gcc_4.9.1/3.2.2/bin",
},
"tool_parameters": {
# "CUTADAPT_PARAMS": "-b AATCTCGTATGCCGTCTTCTGCTTGC -O 3 -m 17 -f fastq",
# "CUTADAPT_PARAMS": "-a CAAGCAGAAGACGGCATACGAGAT -O 3 -m 17 -f fastq",
# "CUTADAPT_PARAMS": "-b CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA -b TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -O 3 -m 17 -f fastq",
"FASTAWITHADAPTERSETD": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.consolidated.fa",
"LEADINGQUALITY": 10,
"TRAILINGQUALITY": 10,
"MINLEN": 17,
"KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"FASTQ_SCREEN_CONFIG2": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen_2.conf",
"CONFMULTIQC": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/multiqc_config.yaml",
"CUTADAPT_PARAMS": "-b CAAGCAGAAGACGGCATACGAGAT -b TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC -O 3 -m 17 -f fastq",
"TRIMMOMATIC": "java -Xmx8g -Djava.io.tmpdir=/scratch -jar /usr/local/apps/trimmomatic/Trimmomatic-0.33/trimmomatic-0.33.jar",
"TRIMMOMATIC.ADAPTERS": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/adapters2.fa",
"MAPPER_PARAMS": "-e -h -q -m -r 5 -u -v -o 4",
"MIRDEEP2_PARAMS": "-P -t Human",
"MIRDEEP2_CLOSE_SPECIES": "none",
"QUANTIFIER_PARAMS": "-P -W",
"BOWTIE_PARAMS": "-p 4 -S -q -n 1 -e 80 -l 30 -a -m 5 --best --strata",
"ADDORREPLACEREADGROUPS_PARAMS": "MAX_RECORDS_IN_RAM=100000 VALIDATION_STRINGENCY=SILENT RGLB=GRCh38 RGCN=NCI RGPL=Illumina ",
"SORTSAM_PARAMS": "MAX_RECORDS_IN_RAM=1800000 VALIDATION_STRINGENCY=SILENT",
"PRINTREADS_PARAMS": "-rf ReassignOneMappingQuality -RMQF 255 -RMQT 60",
"UNIFIEDGENOTYPER_PARAMS": "-glm SNP -dcov 1000",
"HTSEQ_PARAMS": "-m intersection-nonempty -q -t exon -s no",
"QUEUE": "1-day",
},
"memory_parameters": {
"REFERENCE_INDEXES_MEM": "-l h_vmem=3G -l h_stack=10M",
"CUTADAPT_MEM": "-l h_vmem=8G -l h_stack=100M",
"FASTQC_MEM": "-l h_vmem=8G -l h_stack=500M",
"BAMS_MEM": "-l h_vmem=750M -l h_stack=10M",
"MIRDEEP2_MAPPER_MEM": "-l h_vmem=512M -l h_stack=10M",
"MIRDEEP2_MEM": "-l h_vmem=2G -l h_stack=10M",
"VARIANTS_MEM": "-l h_vmem=3G -l h_stack=10M",
"EXPRESSION_REPORTS_MEM": "-l h_vmem=1G -l h_stack=10M",
"DIFF_EXPRESSION_MEM": "-l h_vmem=2G -l h_stack=10M",
"GENCODE_CLASSIFICATION_MEM": "-l h_vmem=3G -l h_stack=10M",
"SAMPLE_SUMMARY_MEM": "-l h_vmem=1G -l h_stack=10M",
"MAIN_DOC_MEM": "-l h_vmem=1G -l h_stack=10M",
},
"java_parameters": {
"CREATEDICTIONARY_JVM_MEM": "-Xmx1g -Xms1g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID",
"ADDORREPLACEREADGROUPS_JVM_MEM": "-Xmx1g -Xms1g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID",
"SORTSAM_JVM_MEM": "-Xmx8g -Xms1g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID",
"UNIFIEDGENOTYPER_JVM_MEM": "-Xmx1g -Xms1g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID",
},
},
}
}